4f6244bd4a
revamped README; not finished yet
2017-10-06 13:02:25 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
84bbc47152
two arrays should be freed with kfree(0,)
...
though in the current code, they are strictly equivalent.
2017-09-23 10:43:22 -04:00
5966e5d6e4
make reader_open() work even if idxopt is NULL
2017-09-15 11:29:49 -04:00
e2823d4aee
r367: index reader optionally writes index
2017-09-14 21:18:13 -04:00
eb00521d9b
redesigned indexing and option APIs
2017-09-14 17:02:01 -04:00
3c91d652dd
r360: allow to set integer max occ
2017-09-13 11:37:00 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
a3c3db6b9b
ONT source code changes to compile with MSVC 14
2017-08-30 16:25:20 +01:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
f81f37fef1
r197: allocate index seq names from kalloc
...
to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
...
Also added index testing API (moved from main.c to index.c)
2017-07-19 10:25:11 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
...
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
a9f089f0aa
r131: wrong EOF test; make mb_size <= batch_size
2017-07-01 09:26:09 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
de54c9dac2
r77: fixed an index loading bug (offset not set)
2017-06-26 13:56:25 -04:00
44cdd18de0
start to work on alignment
2017-06-23 13:44:45 -04:00
d816e48fce
fixed a bug in chaining
2017-06-06 14:33:43 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
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which means there are bugs that need to be fixed
2017-06-06 14:19:50 -04:00
1a9fc04cf0
backup
2017-06-06 10:16:33 -04:00
949d9be872
chaining with DP
2017-05-09 22:20:57 +08:00
7b7fabef4d
added idx_stat
2017-04-26 22:52:28 +08:00
de367a340c
compilable again
2017-04-26 19:36:46 +08:00
56723ad580
moved `sum_len` out of the index
...
as it can be inferred.
2017-04-19 11:06:24 -04:00
f35e152e99
fixed a few memory leaks
2017-04-13 23:05:19 -04:00
9947c953cf
sort positions in each bucket
2017-04-12 13:31:12 -04:00
49b8d23695
indexing not segfault
2017-04-09 14:17:37 -04:00
f5cdd3f72f
is_hpc is a property of the index
2017-04-07 15:42:33 -04:00
b3bc4911ba
index can be compiled; not tested yet
2017-04-07 15:30:30 -04:00
Heng Li
Stefan von Deylen